It's difficult to assertain from your code snippet exactly where you might be having problems.

public class DynamicPanelList {
    public static void main(String[] args) {
        new DynamicPanelList();
    }
    public DynamicPanelList() {
        EventQueue.invokeLater(new Runnable() {
            @Override
            public void run() {
                try {
                    UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
                } catch (Exception ex) {
                }
                JFrame frame = new JFrame("Test");
                frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
                frame.add(new TestPane());
                frame.pack();
                frame.setLocationRelativeTo(null);
                frame.setVisible(true);
            }
        });
    }
    public class TestPane extends JPanel {
        private JPanel mainList;
        public TestPane() {
            setLayout(new BorderLayout());
            mainList = new JPanel(new GridBagLayout());
            GridBagConstraints gbc = new GridBagConstraints();
            gbc.gridwidth = GridBagConstraints.REMAINDER;
            gbc.weightx = 1;
            gbc.weighty = 1;
            mainList.add(new JPanel(), gbc);
            add(new JScrollPane(mainList));
            JButton add = new JButton("Add");
            add.addActionListener(new ActionListener() {
                @Override
                public void actionPerformed(ActionEvent e) {
                    JPanel panel = new JPanel();
                    panel.add(new JLabel("Hello"));
                    panel.setBorder(new MatteBorder(0, 0, 1, 0, Color.GRAY));
                    GridBagConstraints gbc = new GridBagConstraints();
                    gbc.gridwidth = GridBagConstraints.REMAINDER;
                    gbc.weightx = 1;
                    gbc.fill = GridBagConstraints.HORIZONTAL;
                    mainList.add(panel, gbc, 0);
                    validate();
                    repaint();
                }
            });
            add(add, BorderLayout.SOUTH);
        }
        @Override
        public Dimension getPreferredSize() {
            return new Dimension(200, 200);
        }
    }
}
You really need to provide a SSCCE which would allow us to diagnose the problems you are having.
Personally, and this will depend on you requirements, a better layout manager might be VerticalLayout from SwingLabs SwingX libraries.